Governments using COTS operating systems does not imply that these systems are unackable. If the statement of OP would be true, we would just see constant exploitation of RCE zero days, or at the least the impact of that. But that is not the case.

The security profiles of many "flatpacked" applications are quite permissive (see https://flatkill.org/) so that they could be circumvented. Besides that I'm experience some convenience issues when accessing files on my drive. It's especially annoying when using "flatpacked" office such as onlyoffice.

Now that I've read this, I can also remember that I was also annoyed by jerks when scrolling web pages.

I also found the backup management too complicated. I didn't want to back up entire VMs, just the data within the VMs. In principle, I would have had to start up all VMs for backups and run a backup script for each individual VM.

I think it would be good to make it possible to deactivate certain security features such as strict graphics isolation so that users can adjust their settings to their risk acceptance level. It would also be interesting to be able to optionally replace Xen with lighter isolation mechanisms, even if the user would compromise on security here too.